Fix layout of usage blurbs

uf-bare

@@ -26,19 +26,19 @@ err_exit() {
 
 # Function to show usage information and exit
 usage_exit() {
-	echo
-	echo "Usage: $(basename $0) [OPTIONS] [FILE] ..."
-	echo
-	echo "  Output only the bare sequences from each FILE to stanard output, dropping the"
-	echo "  headers.  If no FILE is present or FILE is '-', read from standard input."
-	echo
-	echo "  Options"
-	echo "   -w HDRSFILE   Write the headers to HDRSFILE, which must not already exist."
-	echo "   -f|--force    Overwrite HDRSFILE if it exists."
-	echo 
-	echo "  By default headers go to /dev/null.  Use option -w to store them in a file."
-	echo "  The file can be merged back in with bare sequences using 'uf-dress'."
-	echo
+	echo "
+Usage: $(basename $0) [OPTIONS] [FILE] ...
+
+  Output only the bare sequences from each FILE to standard output, dropping the
+  headers.  If no FILE is present or FILE is '-', read from standard input.
+
+  Options
+   -w HDRSFILE   Write the headers to HDRSFILE, which must not already exist.
+   -f|--force    Overwrite HDRSFILE if it exists.
+
+  By default headers go to /dev/null.  Use option -w to store them in a file.
+  The file can be merged back in with bare sequences using 'uf-dress'.
+" >&2
 	exit ${1:-1}
 }
 

uf-dress

@@ -44,7 +44,7 @@ Usage: $(basename $0) [OPTIONS] [FILE] ...
   $ uf file.fna | uf-bare | ..processing.. | uf-dress -r <(uf file.fna | uf-headers)
 
   See also: 'uf-map' which implements this idiom in a single command.
-"
+" >&2
 	exit ${1:-1}
 }
 

uf-headers

@@ -26,12 +26,12 @@ err_exit() {
 
 # Function to show usage information and exit
 usage_exit() {
-	echo
-	echo "Usage: $(basename $0) [OPTIONS] [FILE] ..."
-	echo
-	echo "  Drop the sequence data and output only the headers from each FILE."
-	echo "  If no FILE is present or FILE is '-', read from standard input."
-	echo 
+	echo "
+Usage: $(basename $0) [OPTIONS] [FILE] ...
+
+  Drop the sequence data and output only the headers from each FILE.
+  If no FILE is present or FILE is '-', read from standard input.
+" >&2
 	exit ${1:-1}
 }
 

uf-map

@@ -26,20 +26,20 @@ err_exit() {
 
 # Function to show usage information and exit
 usage_exit() {
-	echo
-	echo "Usage: $(basename $0) [OPTIONS] OPERATION [FILE] ..."
-	echo
-	echo "  Feed every sequence in FILE to OPERATION's standard input.  When no FILE"
-	echo "  is  present or FILE is '-', read from standard input.  Output is the output"
-	echo "  of OPERATION interspersed with every header from the input."
-	echo
-	echo "  Note that OPERATION is started once, not invoked separately for each line."
-	echo "  It must process every line coming in on its standard input separately."
-	echo
-	echo "  Example"
-	echo "  \$ uf-map 'tr [:upper:] [:lower:]'  # convert all seqs to lower case"
-	echo "  \$ uf-map 'sed -re s,^.{12},,'      # drop initial 12 elements from each"
-	echo 
+	echo "
+Usage: $(basename $0) [OPTIONS] OPERATION [FILE] ...
+
+  Feed every sequence in FILE to OPERATION's standard input.  When no FILE
+  is  present or FILE is '-', read from standard input.  Output is the output
+  of OPERATION interspersed with every header from the input.
+
+  Note that OPERATION is started once, not invoked separately for each line.
+  It must process every line coming in on its standard input separately.
+
+  Example
+  \$ uf-map 'tr [:upper:] [:lower:]'  # convert all seqs to lower case
+  \$ uf-map 'sed -re s,^.{12},,'      # drop initial 12 elements from each
+" >&2
 	exit ${1:-1}
 }
 

uf-random

@@ -30,25 +30,25 @@ err_exit() {
 
 # Function to show usage information and exit
 usage_exit() {
-	echo
-	echo "Usage: $(basename $0) [OPTIONS] [CHARS]"
-	echo
-	echo "  Write to standard output an unfasta file with randomly generated sequences."
-	echo "  Characters are picked randomly uniform from alphabet CHARS (default: $SEQ_CHARS)."
-	echo "  Sequences can be of fixed or random lengths."
-	echo 
-	echo "  Options"
-	echo "   -c|--count COUNT    Number of sequences (default: $SEQ_COUNT)"
-	echo "   -l|--length LEN     Length of sequences (default: $SEQ_LENGTH), excludes -r."
-	echo "   -r|--range MIN,MAX  Random length sequences in range [MIN,MAX], excludes -l."
-	echo 
-	echo "  The CHARS argument can be used to create sequences from any alphabet."
-	echo "  To create biased sequences, repeat characters in CHARS so they have the"
-	echo "  desired proportions.  E.g. \'AACCCTTGGG\' yields sequences with 60% GC."
-	echo
-	echo "  NOTE: the current implementation uses the \$RANDOM builtin to obtain random"
-	echo "  numbers. This is bash specific. TODO: change to read from /dev/urandom."
-	echo
+	echo "
+Usage: $(basename $0) [OPTIONS] [CHARS]
+
+  Write to standard output an unfasta file with randomly generated sequences.
+  Characters are picked randomly uniform from alphabet CHARS (default: $SEQ_CHARS).
+  Sequences can be of fixed or random lengths.
+
+  Options
+   -c|--count COUNT    Number of sequences (default: $SEQ_COUNT)
+   -l|--length LEN     Length of sequences (default: $SEQ_LENGTH), excludes -r.
+   -r|--range MIN,MAX  Random length sequences in range [MIN,MAX], excludes -l.
+
+  The CHARS argument can be used to create sequences from any alphabet.
+  To create biased sequences, repeat characters in CHARS so they have the
+  desired proportions.  E.g. \'AACCCTTGGG\' yields sequences with 60% GC.
+
+  NOTE: the current implementation uses the \$RANDOM builtin to obtain random
+  numbers. This is bash specific. TODO: change to read from /dev/urandom.
+" >&2
 	exit ${1:-1}
 }
 

uf-rc

@@ -37,20 +37,20 @@ err_exit() {
 
 # Function to show usage information and exit
 usage_exit() {
-	echo
-	echo "Usage: $(basename $0) [OPTIONS] [FILE] ..."
-	echo
-	echo "  Write to standard output the reverse complement of every sequence in each FILE."
-	echo "  If no FILE is present or FILE is '-', read from standard input."
-	echo 
-	echo "  Options"
-	echo "   -r|--reverse-only     Reverse only, do not complement."
-	echo "   -c|--complement-only  Complement only, do not reverse."
-	echo "   -m|--mark[-header]    Document operation by attaching '(uf:...)' to headers."
-	echo 
-	echo "  Case is preserved.  Will also work for the degenerate nucleotide letters."
-	echo "  E.g. complement of Y (pyrimidine, T/C) is R (purine, A/T)."
-	echo
+	echo "
+Usage: $(basename $0) [OPTIONS] [FILE] ...
+
+  Write to standard output the reverse complement of every sequence in each FILE.
+  If no FILE is present or FILE is '-', read from standard input.
+
+  Options
+   -r|--reverse-only     Reverse only, do not complement.
+   -c|--complement-only  Complement only, do not reverse.
+   -m|--mark[-header]    Document operation by attaching '(uf:...)' to headers.
+
+  Case is preserved.  Will also work for the degenerate nucleotide letters.
+  E.g. complement of Y (pyrimidine, T/C) is R (purine, A/T).
+" >&2
 	exit ${1:-1}
 }
 

uf-valid

@@ -57,33 +57,33 @@ err_exit() {
 
 # Function to show usage information and exit
 usage_exit() {
-	echo
-	echo "Usage: $(basename $0) [OPTIONS] [FILE] ..."
-	echo
-	echo "  Validate the sequences in each FILE against the allowed alphabet.  If no FILE"
-	echo "  is present or FILE is '-', read from standard input.  Only valid sequences are"
-	echo "  copied to standard output.  For invalid sequences, an error message is printed"
-	echo "  to standard error."
-	echo 
-	echo "  Options"
-	echo "   -a|--allow CHARS  Validate sequences against the alphabet consisting of CHARS."
-	echo "                     May be specified in addition to the synonyms listed below."
-	echo "   -i|--ignore-case  Ignore case for allowed CHARS (default for the synonyms)."
-	echo "   -v|--headers      Validate the syntax of the headers against NCBI conditions."
-	echo "   -s|--stop         Stop processing after the first invalid sequence."
-	echo "   -k|--keep         Do not drop invalid sequences but copy them to standard out."
-	echo "   -q|--quiet        Do not copy standard input to standard output."
-	echo
-	echo "  Synonyms for the usual alphabets (mutually exclusive):"
-	echo "   --dna             Equivalent to: -i -a '$DNA_ALPHABET'"
-	echo "   --rna             Equivalent to: -i -a '$RNA_ALPHABET'"
-	echo "   --nucl            Equivalent to: -i -a '$NUCL_ALPHABET'"
-	echo "   --amino|--prot    Equivalent to: -i -a '$AMINO_ALPHABET'"
-	echo
-	echo "  CAVEAT: when using --allow with symbols other than characters: the current"
-	echo "  implementation is a simple regex search for the complement of the alphabet,"
-	echo "  so symbols which are regex meta-characters like ., ?, and * need escaping."
-	echo 
+	echo "
+Usage: $(basename $0) [OPTIONS] [FILE] ...
+
+  Validate the sequences in each FILE against the allowed alphabet.  If no FILE
+  is present or FILE is '-', read from standard input.  Only valid sequences are
+  copied to standard output.  For invalid sequences, an error message is printed
+  to standard error.
+
+  Options
+   -a|--allow CHARS  Validate sequences against the alphabet consisting of CHARS.
+                     May be specified in addition to the synonyms listed below.
+   -i|--ignore-case  Ignore case for allowed CHARS (default for the synonyms).
+   -v|--headers      Validate the syntax of the headers against NCBI conditions.
+   -s|--stop         Stop processing after the first invalid sequence.
+   -k|--keep         Do not drop invalid sequences but copy them to standard out.
+   -q|--quiet        Do not copy standard input to standard output.
+
+  Synonyms for the usual alphabets (mutually exclusive):
+   --dna             Equivalent to: -i -a '$DNA_ALPHABET'
+   --rna             Equivalent to: -i -a '$RNA_ALPHABET'
+   --nucl            Equivalent to: -i -a '$NUCL_ALPHABET'
+   --amino|--prot    Equivalent to: -i -a '$AMINO_ALPHABET'
+
+  CAVEAT: when using --allow with symbols other than characters: the current
+  implementation is a simple regex search for the complement of the alphabet,
+  so symbols which are regex meta-characters like ., ?, and * need escaping.
+" >&2
 	exit ${1:-1}
 }