def cross_raghavan(file_name, reverse=False):
print "Cross Raghavan running..."
files = [file_name]
our_tables = [(name, "our_files/%s" % name) for name in files]
article_tables = [("s5", "final_format/s5_directed.table"),
("s6", "final_format/s6_directed.table"),
("s7", "final_format/s7_directed.table")]
if not reverse:
TableCrosser(our_tables, article_tables).cross_tables(1000, "results/raghavan")
else:
TableCrosser(our_tables, article_tables).cross_tables_reverse(100000000, "results/raghavan/reverse")
print "Formatting file..."
TableFormatter.split_reverse_rows(TableLoader, "results/raghavan/reverse/%s.table" % file_name)
print "Done."
def cross_bilusic(file_name, reverse=False):
print "Cross Bilusic running..."
files = [file_name]
our_tables = [(name, "our_files/%s" % name) for name in files]
article_tables = [("2014RNABIOL0069R_TableS1", "bilusic/final/2014RNABIOL0069R_TableS1.table"),
("2014RNABIOL0069R_TableS2", "bilusic/final/2014RNABIOL0069R_TableS2.table"),
("2014RNABIOL0069R_TableS3", "bilusic/final/2014RNABIOL0069R_TableS3.table"),
("2014RNABIOL0069R_TableS4", "bilusic/final/2014RNABIOL0069R_TableS4.table")]
if not reverse:
TableCrosser(our_tables, article_tables).cross_tables(1000, "results/bilusic", 20)
else:
TableCrosser(our_tables, article_tables).cross_tables_reverse(100000000, "results/bilusic/reverse", 20)
print "Formatting file..."
TableFormatter.split_reverse_rows(TableLoader, "results/bilusic/reverse/%s.table" % file_name)
print "Done."
def cross_zhang(file_name, reverse=False):
print "Cross Zhang running..."
files = [file_name]
our_tables = [(name, "our_files/%s" % name) for name in files]
article_tables = [("zhang2013_s3_sheet_2008", "zhang/final/Table-s3-zhang-2013-sheet2008.table"),
("zhang2013_s3_sheet_2009", "zhang/final/Table-s3-zhang-2013-sheet2009.table"),
("zhang2013_s4_sheet_2008", "zhang/final/Table-s4-zhang-2013-sheet2008.table"),
("zhang2013_s4_sheet_2009", "zhang/final/Table-s4-zhang-2013-sheet2009.table")]
if not reverse:
TableCrosser(our_tables, article_tables).cross_tables(1000, "results/zhang")
else:
TableCrosser(our_tables, article_tables).cross_tables_reverse(100000000, "results/zhang/reverse")
print "Formatting file..."
TableFormatter.split_reverse_rows(TableLoader, "results/zhang/reverse/%s.table" % file_name)
print "Done."
files = [
"assign-type-to-all-chimeras-of-Iron_limitation_CL_FLAG207_208_305_all_fragments_l25.txt_all_interactions.with-type",
"assign-type-to-all-chimeras-of-Log_phase_CL_FLAG101-104_108_109_all_fragments_l25.txt_all_interactions.with-type",
"assign-type-to-all-chimeras-of-MG_hfq-WT101_cutadapt_bwa.bam_all_fragments_l25.txt_all_interactions.with-type",
"assign-type-to-all-chimeras-of-MG_hfq-wt202_CL_Stationary_cutadapt_bwa.bam_all_fragments_l25.txt_all_interactions.with-type",
"assign-type-to-all-chimeras-of-Stationary_CL_FLAG209_210_312_all_fragments_l25.txt_all_interactions.with-type",
"assign-type-to-signif-chimeras-of-Iron_limitation_CL_FLAG207_208_305_all_fragments_l25.txt_sig_interactions.with-type",
"assign-type-to-signif-chimeras-of-Log_phase_CL_FLAG101-104_108_109_all_fragments_l25.txt_sig_interactions.with-type",
"assign-type-to-signif-chimeras-of-Stationary_CL_FLAG209_210_312_all_fragments_l25.txt_sig_interactions.with-type",
"assign-type-to-single-counts-of-Iron_limitation_CL_FLAG207_208_305_all_fragments_l25.txt_single_counts.with-type",
"assign-type-to-single-counts-of-Log_phase_CL_FLAG101-104_108_109_all_fragments_l25.txt_single_counts.with-type",
"assign-type-to-single-counts-of-MG_hfq-WT101_cutadapt_bwa.bam_all_fragments_l25.txt_single_counts.with-type",
"assign-type-to-single-counts-of-MG_hfq-wt202_CL_Stationary_cutadapt_bwa.bam_all_fragments_l25.txt_single_counts.with-type",
"assign-type-to-single-counts-of-Stationary_CL_FLAG209_210_312_all_fragments_l25.txt_single_counts.with-type",
]
from TableCrosser import cross_zhang, cross_raghavan, cross_bilusic, cross_tss, cross_lybecker
from TableFormatter import TableFormatter
from TableLoader import TableLoader
for name in files:
print name
print "*" * 100
# TableFormatter.split_reverse_rows(TableLoader, "results/raghavan/reverse/%s.table" % name)
# TableFormatter.split_reverse_rows(TableLoader, "results/zhang/reverse/%s.table" % name)
TableFormatter.split_reverse_rows(TableLoader, "results/bilusic/reverse/%s.table" % name)
# TableFormatter.split_reverse_rows(TableLoader, "results/tss/reverse/%s.table" % name)
# TableFormatter.split_reverse_rows(TableLoader, "results/lybecker/reverse/%s.table" % name)
files = [
"assign-type-to-all-chimeras-of-Iron_limitation_CL_FLAG207_208_305_all_fragments_l25.txt_all_interactions.with-type",
"assign-type-to-all-chimeras-of-Log_phase_CL_FLAG101-104_108_109_all_fragments_l25.txt_all_interactions.with-type",
"assign-type-to-all-chimeras-of-MG_hfq-WT101_cutadapt_bwa.bam_all_fragments_l25.txt_all_interactions.with-type",
"assign-type-to-all-chimeras-of-MG_hfq-wt202_CL_Stationary_cutadapt_bwa.bam_all_fragments_l25.txt_all_interactions.with-type",
"assign-type-to-all-chimeras-of-Stationary_CL_FLAG209_210_312_all_fragments_l25.txt_all_interactions.with-type",
"assign-type-to-signif-chimeras-of-Iron_limitation_CL_FLAG207_208_305_all_fragments_l25.txt_sig_interactions.with-type",
"assign-type-to-signif-chimeras-of-Log_phase_CL_FLAG101-104_108_109_all_fragments_l25.txt_sig_interactions.with-type",
"assign-type-to-signif-chimeras-of-Stationary_CL_FLAG209_210_312_all_fragments_l25.txt_sig_interactions.with-type",
"assign-type-to-single-counts-of-Iron_limitation_CL_FLAG207_208_305_all_fragments_l25.txt_single_counts.with-type",
"assign-type-to-single-counts-of-Log_phase_CL_FLAG101-104_108_109_all_fragments_l25.txt_single_counts.with-type",
"assign-type-to-single-counts-of-MG_hfq-WT101_cutadapt_bwa.bam_all_fragments_l25.txt_single_counts.with-type",
"assign-type-to-single-counts-of-MG_hfq-wt202_CL_Stationary_cutadapt_bwa.bam_all_fragments_l25.txt_single_counts.with-type",
"assign-type-to-single-counts-of-Stationary_CL_FLAG209_210_312_all_fragments_l25.txt_single_counts.with-type"
]
from TableCrosser import cross_zhang, cross_raghavan, cross_bilusic, cross_tss, cross_lybecker
from TableFormatter import TableFormatter
from TableLoader import TableLoader
for name in files:
print name
print "*" * 100
# TableFormatter.split_reverse_rows(TableLoader, "results/raghavan/reverse/%s.table" % name)
# TableFormatter.split_reverse_rows(TableLoader, "results/zhang/reverse/%s.table" % name)
TableFormatter.split_reverse_rows(
TableLoader, "results/bilusic/reverse/%s.table" % name)
# TableFormatter.split_reverse_rows(TableLoader, "results/tss/reverse/%s.table" % name)
# TableFormatter.split_reverse_rows(TableLoader, "results/lybecker/reverse/%s.table" % name)
