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remove the usage of hast tables in the fasta-tools

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This commit is contained in:
Wen-Yu Chung
2009-01-19 15:47:02 -05:00
parent 4bb40fba54
commit 498fbac868
3 changed files with 80 additions and 78 deletions
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tools/fasta_tools/fasta_compute_length.py
+23 -27
View File
@@ -1,8 +1,8 @@
#! /usr/bin/python
"""
Input: fasta, minimal length, maximal length
Output: fasta
Return sequences whose lengths are within the range.
Input: fasta, int
Output: tabular
Return titles with lengths of corresponding seq
"""
import sys, os
@@ -10,41 +10,37 @@ import sys, os
assert sys.version_info[:2] >= ( 2, 4 )
def __main__():
input_filename = sys.argv[1]
output_filename = sys.argv[2]
infile = sys.argv[1]
outfile = sys.argv[2]
keep_first = int( sys.argv[3] )
tmp_title = tmp_seq = ''
tmp_seq_count = 0
seq_hash = {}
fasta_title = fasta_seq = ''
# number of char to keep in the title
if keep_first == 0:
keep_first = None
else:
keep_first += 1
for i, line in enumerate( file( input_filename ) ):
out = open(outfile, 'w')
for i, line in enumerate( file( infile ) ):
line = line.rstrip( '\r\n' )
if not line or line.startswith( '#' ):
continue
if line[0] == '>':
if len( tmp_seq ) > 0:
tmp_seq_count += 1
seq_hash[ ( tmp_seq_count, tmp_title ) ] = tmp_seq
tmp_title = line
tmp_seq = ''
if len( fasta_seq ) > 0 :
out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first ], len( fasta_seq ) ) )
fasta_title = line
fasta_seq = ''
else:
tmp_seq = "%s%s" % ( tmp_seq, line )
if line.split() and line.split()[0].isdigit():
tmp_seq = "%s " % tmp_seq
if len( tmp_seq ) > 0:
seq_hash[ ( tmp_seq_count, tmp_title ) ] = tmp_seq
title_keys = seq_hash.keys()
title_keys.sort()
output_handle = open( output_filename, 'w' )
for i, fasta_title in title_keys:
tmp_seq = seq_hash[ ( i, fasta_title ) ]
output_handle.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first ], len( tmp_seq ) ) )
output_handle.close()
fasta_seq = "%s%s" % ( fasta_seq, line )
# check the last sequence
if len( fasta_seq ) > 0:
out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first ], len( fasta_seq ) ) )
out.close()
if __name__ == "__main__" : __main__()
tools/fasta_tools/fasta_filter_by_length.py
+41 -28
View File
@@ -15,7 +15,7 @@ def stop_err( msg ):
def __main__():
input_filename = sys.argv[1]
infile = sys.argv[1]
try:
min_length = int( sys.argv[2] )
except:
@@ -24,49 +24,62 @@ def __main__():
max_length = int( sys.argv[3] )
except:
stop_err( "Maximum length of the return sequence requires a numerical value." )
output_filename = sys.argv[4]
tmp_title = tmp_seq = ''
tmp_seq_count = 0
seq_hash = {}
outfile = sys.argv[4]
fasta_title = fasta_seq = ''
at_least_one = 0
out = open( outfile, 'w' )
for i, line in enumerate( file( input_filename ) ):
for i, line in enumerate( file( infile ) ):
line = line.rstrip( '\r\n' )
if not line or line.startswith( '#' ):
continue
if line[0] == '>':
if len( tmp_seq ) > 0:
tmp_seq_count += 1
seq_hash[ ( tmp_seq_count, tmp_title ) ] = tmp_seq
tmp_title = line
tmp_seq = ''
if len( fasta_seq ) > 0:
if max_length <= 0:
compare_max_length = len( fasta_seq ) + 1
else:
compare_max_length = max_length
l = len( fasta_seq )
if l >= min_length and l <= compare_max_length:
at_least_one += 1
out.write( "%s\n" % fasta_title )
c = 0
s = fasta_seq
while c < l:
b = min( c + 50, l )
out.write( "%s\n" % s[ c:b ] )
c = b
fasta_title = line
fasta_seq = ''
else:
tmp_seq = "%s%s" % ( tmp_seq, line )
if line.split()[0].isdigit():
tmp_seq = "%s " % tmp_seq
if len( tmp_seq ) > 0:
seq_hash[ ( tmp_seq_count, tmp_title ) ] = tmp_seq
fasta_seq = "%s%s" % ( fasta_seq, line )
title_keys = seq_hash.keys()
title_keys.sort()
output_handle = open( output_filename, 'w' )
at_least_one = 0
for i, fasta_title in title_keys:
tmp_seq = seq_hash[ ( i, fasta_title ) ]
if len( fasta_seq ) > 0:
if max_length <= 0:
compare_max_length = len( tmp_seq ) + 1
compare_max_length = len( fasta_seq ) + 1
else:
compare_max_length = max_length
l = len( tmp_seq )
l = len( fasta_seq )
if l >= min_length and l <= compare_max_length:
at_least_one += 1
output_handle.write( "%s\n" % fasta_title )
out.write( "%s\n" % fasta_title )
c = 0
s = tmp_seq
s = fasta_seq
while c < l:
b = min( c + 50, l )
output_handle.write( "%s\n" % s[ c:b ] )
out.write( "%s\n" % s[ c:b ] )
c = b
output_handle.close()
out.close()
if at_least_one == 0:
print "There is no sequence that falls within your range."
tools/fasta_tools/fasta_to_tabular.py
+16 -23
View File
@@ -1,9 +1,9 @@
#! /usr/bin/python
# This code exists in 2 places: ~/datatypes/converters and ~/tools/fasta_tools
"""
Input: fasta, minimal length, maximal length
Output: fasta
Return sequences whose lengths are within the range.
Input: fasta, int
Output: tabular
format convert: fasta to tabular
"""
import sys, os
@@ -14,38 +14,31 @@ def __main__():
infile = sys.argv[1]
outfile = sys.argv[2]
keep_first = int( sys.argv[3] )
title = ''
sequence = ''
sequence_count = 0
fasta_title = fasta_seq = ''
if keep_first == 0:
keep_first = None
else:
keep_first += 1
out = open( outfile, 'w' )
for i, line in enumerate( open( infile ) ):
line = line.rstrip( '\r\n' )
if not line or line.startswith( '#' ):
continue
if line.startswith( '>' ):
if sequence:
sequence_count += 1
seq_hash[( sequence_count, title )] = sequence
title = line
sequence = ''
if fasta_seq:
out.write( "%s\t%s\n" %( fasta_title[ 1:keep_first ], fasta_seq ) )
fasta_title = line
fasta_seq = ''
else:
sequence = "%s%s" % ( sequence, line )
if line.split() and line.split()[0].isdigit():
sequence += ' '
if sequence:
seq_hash[( sequence_count, title )] = sequence
# return only those lengths are in the range
title_keys = seq_hash.keys()
title_keys.sort()
out = open( outfile, 'w' )
for i, fasta_title in title_keys:
sequence = seq_hash[( i, fasta_title )]
out.write( "%s\t%s\n" %( fasta_title[ 1:keep_first ], sequence ) )
if line:
fasta_seq = "%s%s" % ( fasta_seq, line )
if fasta_seq:
out.write( "%s\t%s\n" %( fasta_title[ 1:keep_first ], fasta_seq ) )
out.close()
if __name__ == "__main__" : __main__()